(GOSemSim package) secondary GO terms generating NA values
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@lwillianpacheco-18611
Last seen 19 months ago
Brazil/Rio de Janeiro/UFRJ

Dear all,

I'm using GOSemSim for computing semantic similarities between GO terms.

When I performed the similarity analysis with Wang method there are no problem:

> library("GOSemSim")

> hsGOBP <- godata('org.Hs.eg.db', ont="BP")
preparing gene to GO mapping data...
preparing IC data...

> goSim("GO:0042346", "GO:0042346", semData=hsGOBP, measure="Wang")
[1] 1

But if I change the method to Resnik, Rel, Jiang or Lin, the analysis generate only one NA as result:

> goSim("GO:0042346", "GO:0042346", semData=hsGOBP, measure="Rel")
[1] NA

Manipulating the vector I discovered that the error is produced by secondary GO term, GO:0042346 (above).

Are there an alternative to analyze a vector with secondary GO terms?

 

Thanks Luis Arge

 

--

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=pt_BR.UTF-8       LC_NUMERIC=C               LC_TIME=pt_BR.UTF-8       
 [4] LC_COLLATE=pt_BR.UTF-8     LC_MONETARY=pt_BR.UTF-8    LC_MESSAGES=pt_BR.UTF-8   
 [7] LC_PAPER=pt_BR.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] org.Hs.eg.db_3.7.0   AnnotationDbi_1.44.0 IRanges_2.16.0       S4Vectors_0.20.1    
[5] Biobase_2.42.0       BiocGenerics_0.28.0  GOSemSim_2.8.0      

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0      GO.db_3.7.0     digest_0.6.18   DBI_1.0.0       RSQLite_2.1.1  
 [6] blob_1.1.1      tools_3.5.1     bit64_0.9-7     bit_1.1-14      compiler_3.5.1
[11] pkgconfig_2.0.2 memoise_1.1.0 

gosemsim • 509 views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…
because IC-based methods are species-specific and the GO term is not valid for human. > require(org.Hs.eg.db) > get('GO:0042346', org.Hs.egGO2EG) Error in .checkKeys(value, Rkeys(x), x@ifnotfound) : value for "GO:0042346" not found On Sat, Dec 1, 2018 at 1:05 AM l.willianpacheco [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User l.willianpacheco <https: support.bioconductor.org="" u="" 18611=""/> wrote Question: > (GOSemSim package) secondary GO terms generating NA values > <https: support.bioconductor.org="" p="" 115680=""/>: > > Dear all, > > I'm using GOSemSim for computing semantic similarities between GO terms. > > When I performed the similarity analysis with Wang method there are no > problem: > > > library("GOSemSim") > > > hsGOBP <- godata('org.Hs.eg.db', ont="BP") > preparing gene to GO mapping data... > preparing IC data... > > > goSim("GO:0042346", "GO:0042346", semData=hsGOBP, measure="Wang") > [1] 1 > > But if I change the method to Resnik, Rel, Jiang or Lin, the analysis > generate only one NA as result: > > > goSim("GO:0042346", "GO:0042346", semData=hsGOBP, measure="Rel") > [1] NA > > Manipulating the vector I discovered that the error is produced by > secondary GO term, GO:0042346 (above). > > Are there an alternative to analyze a vector with secondary GO terms? > > > > Thanks Luis Arge > > > > -- > > > sessionInfo() > R version 3.5.1 (2018-07-02) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 16.04.5 LTS > > Matrix products: default > BLAS: /usr/lib/openblas-base/libblas.so.3 > LAPACK: /usr/lib/libopenblasp-r0.2.18.so > > locale: > [1] LC_CTYPE=pt_BR.UTF-8 LC_NUMERIC=C > LC_TIME=pt_BR.UTF-8 > [4] LC_COLLATE=pt_BR.UTF-8 LC_MONETARY=pt_BR.UTF-8 > LC_MESSAGES=pt_BR.UTF-8 > [7] LC_PAPER=pt_BR.UTF-8 LC_NAME=C > LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=pt_BR.UTF-8 > LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats4 stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] org.Hs.eg.db_3.7.0 AnnotationDbi_1.44.0 IRanges_2.16.0 > S4Vectors_0.20.1 > [5] Biobase_2.42.0 BiocGenerics_0.28.0 GOSemSim_2.8.0 > > loaded via a namespace (and not attached): > [1] Rcpp_1.0.0 GO.db_3.7.0 digest_0.6.18 DBI_1.0.0 > RSQLite_2.1.1 > [6] blob_1.1.1 tools_3.5.1 bit64_0.9-7 bit_1.1-14 > compiler_3.5.1 > [11] pkgconfig_2.0.2 memoise_1.1.0 > ------------------------------ > > Post tags: gosemsim > > You may reply via email or visit > (GOSemSim package) secondary GO terms generating NA values > -- --~--~---------~--~----~------------~-------~--~----~ Guangchuang Yu PhD Professor School of Basic Medical Sciences Southern Medical University Guangzhou, China www: https://guangchuangyu.github.io -~----------~----~----~----~------~----~------~--~---
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Thank you Guangchuang.

I'll verify all GO terms and then replace by their primary GO.

--

Luis Arge

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